#include <SecondaryStructureSelector.hh>

Inheritance diagram for core::select::residue_selector::SecondaryStructureSelector:

Public Member Functions
	SecondaryStructureSelector ()

	SecondaryStructureSelector (std::string const &selected)

ResidueSelectorOP	clone () const override
	Clone operator. More...

	~SecondaryStructureSelector () override

ResidueSubset	apply (core::pose::Pose const &pose) const override
	Return a ResidueSubset indicating a selection of Residues from the input Pose; the ResidueSubset is an array of booleans where a value of "true" for position i indicates that residue i is a part of the selected subset – and a value of "false" would indicate that it is not. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap) override
	Initialize any data members of this instance from an input tag and a DataMap object. More...

std::string	get_name () const override

void	set_overlap (core::Size const overlapval)
	sets number of residues around the given SS elements to select (default=0) More...

void	set_minH (core::Size const minHval)
	sets the minimal number of consecutive H residues to keep the secondary structure assignation (default=1) More...

void	set_minE (core::Size const minEval)
	sets the minimal number of consecutive E residues to keep the secondary structure assignation (default=1) More...

void	set_selected_ss (std::string const &selected)
	sets ss characters to select – must be set prior to apply() More...

void	set_include_terminal_loops (bool const inc_term)
	if true, one-residue terminal "loops" will be included (default=false) More...

void	set_pose_secstruct (std::string const &ss)
	Override pose secondary structure. The secondary structure set by this method will always be used if it is non-empty. More...

void	set_use_dssp (bool const use_dssp)
	If set, dssp will be used to determine secondary structure. Has no effect if pose_secstruct_ is set. More...

Public Member Functions inherited from core::select::residue_selector::ResidueSelector
	ResidueSelector ()
	Constructor. More...

	~ResidueSelector () override
	Destructor. More...

utility::vector1< core::Size >	selection_positions (core::pose::Pose const &pose) const
	Calls apply and returns the Rosetta numbering corresponding to the selected residues. More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static std::string	class_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Private Member Functions
std::string	get_secstruct (core::pose::Pose const &pose) const
	gets the secondary structure to be used by the selector More...

void	fix_secstruct_definition (std::string &ss) const
	fixes the secondary structure according to the expected minimal length of each secondary structure. More...

void	add_overlap (ResidueSubset &matching_ss, pose::Pose const &pose, std::string const &ss) const

bool	check_ss (std::string const &ss) const

Private Attributes
std::string	pose_secstruct_

core::Size	overlap_

core::Size	minH_

core::Size	minE_

bool	include_terminal_loops_

bool	use_dssp_

std::set< char >	selected_ss_

Constructor & Destructor Documentation

◆ SecondaryStructureSelector() [1/2]

core::select::residue_selector::SecondaryStructureSelector::SecondaryStructureSelector ( )

References selected_ss_.

◆ SecondaryStructureSelector() [2/2]

core::select::residue_selector::SecondaryStructureSelector::SecondaryStructureSelector ( std::string const & selected )

References check_ss(), and set_selected_ss().

◆ ~SecondaryStructureSelector()

core::select::residue_selector::SecondaryStructureSelector::~SecondaryStructureSelector ( )

overridedefault

Member Function Documentation

◆ add_overlap()

void core::select::residue_selector::SecondaryStructureSelector::add_overlap	(	ResidueSubset &	matching_ss,
		pose::Pose const &	pose,
		std::string const &	ss
	)		const

private

References include_terminal_loops_, overlap_, core::pose::pose_residue_is_terminal(), protocols::sic_dock::range(), and core::select::residue_selector::TR().

Referenced by apply().

◆ apply()

ResidueSubset core::select::residue_selector::SecondaryStructureSelector::apply ( core::pose::Pose const & pose ) const

overridevirtual

Return a ResidueSubset indicating a selection of Residues from the input Pose; the ResidueSubset is an array of booleans where a value of "true" for position i indicates that residue i is a part of the selected subset – and a value of "false" would indicate that it is not.

Implements core::select::residue_selector::ResidueSelector.

References add_overlap(), check_ss(), fix_secstruct_definition(), get_secstruct(), selected_ss_, core::pose::Pose::size(), and core::select::residue_selector::TR().

Referenced by protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator::apply().

◆ check_ss()

bool core::select::residue_selector::SecondaryStructureSelector::check_ss ( std::string const & ss ) const

private

Referenced by apply(), parse_my_tag(), and SecondaryStructureSelector().

◆ class_name()

std::string core::select::residue_selector::SecondaryStructureSelector::class_name ( )

static

Referenced by get_name(), core::select::residue_selector::SecondaryStructureSelectorCreator::keyname(), and provide_xml_schema().

◆ clone()

ResidueSelectorOP core::select::residue_selector::SecondaryStructureSelector::clone ( ) const

overridevirtual

Clone operator.

Copy this object and return an owning pointer to the new object.

Implements core::select::residue_selector::ResidueSelector.

◆ fix_secstruct_definition()

void core::select::residue_selector::SecondaryStructureSelector::fix_secstruct_definition ( std::string & ss ) const

private

fixes the secondary structure according to the expected minimal length of each secondary structure.

Parameters

[in] ss string with the secondary structure definition

References minE_, minH_, and core::select::residue_selector::TR().

Referenced by apply().

◆ get_name()

std::string core::select::residue_selector::SecondaryStructureSelector::get_name ( ) const

overridevirtual

Implements core::select::residue_selector::ResidueSelector.

References class_name().

◆ get_secstruct()

std::string core::select::residue_selector::SecondaryStructureSelector::get_secstruct ( core::pose::Pose const & pose ) const

private

gets the secondary structure to be used by the selector

Parameters

[in] pose Input pose

Determines secondary structure by the following rules:

If pose_secstruct_ is user-specified, use that
If use_dssp_ is true, run DSSP and use DSSP secstruct
If use_dssp_ is false, return pose.secstruct()

References protocols::simple_filters::dssp(), pose_secstruct_, core::pose::Pose::secstruct(), core::select::residue_selector::TR(), and use_dssp_.

Referenced by apply().

◆ parse_my_tag()

void core::select::residue_selector::SecondaryStructureSelector::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datacache
	)

overridevirtual

Initialize any data members of this instance from an input tag and a DataMap object.

Noop implementation in the base class in the case that a derived class has no need to read data from an input tag

Reimplemented from core::select::residue_selector::ResidueSelector.

References check_ss(), include_terminal_loops_, minE_, minH_, overlap_, pose_secstruct_, set_include_terminal_loops(), set_minE(), set_minH(), set_overlap(), set_pose_secstruct(), set_selected_ss(), set_use_dssp(), and use_dssp_.

◆ provide_xml_schema()

void core::select::residue_selector::SecondaryStructureSelector::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References class_name(), and core::select::residue_selector::xsd_type_definition_w_attributes().

Referenced by core::select::residue_selector::SecondaryStructureSelectorCreator::provide_xml_schema().

◆ set_include_terminal_loops()

void core::select::residue_selector::SecondaryStructureSelector::set_include_terminal_loops ( bool const inc_term )

if true, one-residue terminal "loops" will be included (default=false)

References include_terminal_loops_.

Referenced by parse_my_tag().

◆ set_minE()

void core::select::residue_selector::SecondaryStructureSelector::set_minE ( core::Size const minEval )

sets the minimal number of consecutive E residues to keep the secondary structure assignation (default=1)

References minE_.

Referenced by protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator::apply(), and parse_my_tag().

◆ set_minH()

void core::select::residue_selector::SecondaryStructureSelector::set_minH ( core::Size const minHval )

sets the minimal number of consecutive H residues to keep the secondary structure assignation (default=1)

References minH_.

Referenced by parse_my_tag().

◆ set_overlap()

void core::select::residue_selector::SecondaryStructureSelector::set_overlap ( core::Size const overlapval )

sets number of residues around the given SS elements to select (default=0)

References overlap_.

Referenced by parse_my_tag().

◆ set_pose_secstruct()

void core::select::residue_selector::SecondaryStructureSelector::set_pose_secstruct ( std::string const & ss )

Override pose secondary structure. The secondary structure set by this method will always be used if it is non-empty.

References pose_secstruct_.

Referenced by parse_my_tag().

◆ set_selected_ss()

void core::select::residue_selector::SecondaryStructureSelector::set_selected_ss ( std::string const & selected )

sets ss characters to select – must be set prior to apply()

References selected_ss_.

Referenced by parse_my_tag(), and SecondaryStructureSelector().

◆ set_use_dssp()

void core::select::residue_selector::SecondaryStructureSelector::set_use_dssp ( bool const use_dssp )

If set, dssp will be used to determine secondary structure. Has no effect if pose_secstruct_ is set.

Determines secondary structure by the following rules:

If pose_secstruct_ is user-specified, use that
If use_dssp_ is true, run DSSP and use DSSP secstruct
If use_dssp_ is false, return pose.secstruct()

References use_dssp_.

Referenced by parse_my_tag().

Member Data Documentation

◆ include_terminal_loops_

bool core::select::residue_selector::SecondaryStructureSelector::include_terminal_loops_

private

Referenced by add_overlap(), parse_my_tag(), and set_include_terminal_loops().

◆ minE_

core::Size core::select::residue_selector::SecondaryStructureSelector::minE_

private

Referenced by fix_secstruct_definition(), parse_my_tag(), and set_minE().

◆ minH_

core::Size core::select::residue_selector::SecondaryStructureSelector::minH_

private

Referenced by fix_secstruct_definition(), parse_my_tag(), and set_minH().

◆ overlap_

core::Size core::select::residue_selector::SecondaryStructureSelector::overlap_

private

Referenced by add_overlap(), parse_my_tag(), and set_overlap().

◆ pose_secstruct_

std::string core::select::residue_selector::SecondaryStructureSelector::pose_secstruct_

private

Referenced by get_secstruct(), parse_my_tag(), and set_pose_secstruct().

◆ selected_ss_

std::set< char > core::select::residue_selector::SecondaryStructureSelector::selected_ss_

private

Referenced by apply(), SecondaryStructureSelector(), and set_selected_ss().

◆ use_dssp_

bool core::select::residue_selector::SecondaryStructureSelector::use_dssp_

private

Referenced by get_secstruct(), parse_my_tag(), and set_use_dssp().

The documentation for this class was generated from the following files:

src/core/select/residue_selector/SecondaryStructureSelector.hh
src/core/select/residue_selector/SecondaryStructureSelector.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ SecondaryStructureSelector() [1/2]

◆ SecondaryStructureSelector() [2/2]

◆ ~SecondaryStructureSelector()

Member Function Documentation

◆ add_overlap()

◆ apply()

◆ check_ss()

◆ class_name()

◆ clone()

◆ fix_secstruct_definition()

◆ get_name()

◆ get_secstruct()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ set_include_terminal_loops()

◆ set_minE()

◆ set_minH()

◆ set_overlap()

◆ set_pose_secstruct()

◆ set_selected_ss()

◆ set_use_dssp()

Member Data Documentation

◆ include_terminal_loops_

◆ minE_

◆ minH_

◆ overlap_

◆ pose_secstruct_

◆ selected_ss_

◆ use_dssp_